Transcriptome analysis around the onset of strawberry fruit ripening uncovers an important role of oxidative phosphorylation in ripening

Abscisic acid controls sugar accumulation essential to strawberry fruit ripening via the FaRIPK1-FaTCP7-FaSTP13/FaSPT module

Strawberry is considered as a model plant for studying the ripening of abscisic acid (ABA)-regulated non-climacteric fruits, a process in which sugar plays a fundamental role, while how ABA regulates sugar accumulation remains unclear. This study provides a direct line of physiological, biochemical, and molecular evidence that ABA signaling regulates sugar accumulation via the FaRIPK1-FaTCP7-FaSTP13/FaSPT signaling pathway. Herein, FaRIPK1, a red-initial protein kinase 1 previously identified in strawberry fruit, not only interacted with the transcription factor FaTCP7 (TEOSINTE BRANCHEN 1, CYCLOIDEA, and PCF) but also phosphorylated the critical Ser89 and Thr93 sites of FaTCP7, which negatively regulated strawberry fruit ripening, as evidenced by the transient overexpression (OE) and virus-induced gene silencing transgenic system. Furthermore, the DAP-seq experiments revealed that FvTCP7 bound the motif "GTGGNNCCCNC" in the promoters of two sugar transporter genes, FaSTP13 (sugar transport protein 13) and FaSPT (sugar phosphate/phosphate translocator), inhibiting their transcription activities as determined by the electrophoretic mobility shift assay, yeast one-hybrid, and dual-luciferase reporter assays. The downregulated FaSTP13 and FaSPT transcripts in the FaTCP7-OE fruit resulted in a reduction in soluble sugar content. Consistently, the yeast absorption test revealed that the two transporters had hexose transport activity. Especially, the phosphorylation-inhibited binding of FaTCP7 to the promoters of FaSTP13 and FaSPT could result in the release of their transcriptional activities. In addition, the phosphomimetic form FaTCP7S89D or FaTCP7T93D could rescue the phenotype of FaTCP7-OE fruits. Importantly, exogenous ABA treatment enhanced the FaRIPK1-FaTCP7 interaction. Overall, we found direct evidence that ABA signaling controls sugar accumulation during strawberry fruit ripening via the "FaRIPK1-FaTCP7-FaSTP13/FaSPT" module.

Tissue-specific proteome profile analysis reveals regulatory and stress responsive networks in passion fruit during storage

Passiflora edulis, commonly known as passion fruit, is a crop with a fragrant aroma and refreshingly tropical flavor that is a valuable source of antioxidants. It offers a unique opportunity for growers because of its adaptability to tropical and subtropical climates. Passion fruit can be sold in the fresh market or used in value-added products, but its postharvest shelf life has not been well-researched, nor have superior cultivars been well-developed. Understanding the proteins expressed at the tissue level during the postharvest stage can help improve fruit quality and extend shelf life. In this study, we carried out comparative proteomics analysis on four passion fruit tissues, the epicarp, mesocarp, endocarp, and pulp, using multiplexed isobaric tandem mass tag (TMT) labeling quantitation. A total of 3352 proteins were identified, including 295 differentially expressed proteins (DEPs). Of these DEPs, 213 showed a fold increase greater than 1.45 (50 proteins) or a fold decrease less than 0.45 (163 proteins) with different patterns among tissue types. Among the DEPs, there were proteins expressed with functions in oxygen scavenging, lipid peroxidation, response to heat stress, and pathogen resistance. Thirty-six proteins were designated as hypothetical proteins were characterized for potential functions in immunity, cell structure, homeostasis, stress response, protein metabolism and miraculin biosynthesis. This research provides insight into tissue-specific pathways that can be further studied within fruit physiology and postharvest shelf life to aid in implementing effective plant breeding programs. Knowing the tissue-specific function of fruit is essential for improving fruit quality, developing new varieties, identifying health benefits, and optimizing processing techniques.

Integrating the multiple functions of CHLH into chloroplast-derived signaling fundamental to plant development and adaptation as well as fruit ripening

Chlorophyll (Chl)-mediated oxygenic photosynthesis sustains life on Earth. Greening leaves play fundamental roles in plant growth and crop yield, correlating with the idea that more Chls lead to better adaptation. However, they face significant challenges from various unfavorable environments. Chl biosynthesis hinges on the first committed step, which involves inserting Mg2+ into protoporphyrin. This step is facilitated by the H subunit of magnesium chelatase (CHLH) and features a conserved mechanism from cyanobacteria to plants. For better adaptation to fluctuating land environments, especially drought, CHLH evolves multiple biological functions, including Chl biosynthesis, retrograde signaling, and abscisic acid (ABA) responses. Additionally, it integrates into various chloroplast-derived signaling pathways, encompassing both retrograde signaling and hormonal signaling. The former comprises ROS (reactive oxygen species), heme, GUN (genomes uncoupled), MEcPP (methylerythritol cyclodiphosphate), β-CC (β-cyclocitral), and PAP (3'-phosphoadenosine-5'-phosphate). The latter involves phytohormones like ABA, ethylene, auxin, cytokinin, gibberellin, strigolactone, brassinolide, salicylic acid, and jasmonic acid. Together, these elements create a coordinated regulatory network tailored to plant development and adaptation. An intriguing example is how drought-mediated improvement of fruit quality provides insights into chloroplast-derived signaling, aiding the shift from vegetative to reproductive growth. In this context, we explore the integration of CHLH's multifaceted roles into chloroplast-derived signaling, which lays the foundation for plant development and adaptation, as well as fruit ripening and quality. In the future, manipulating chloroplast-derived signaling may offer a promising avenue to enhance crop yield and quality through the homeostasis, function, and regulation of Chls.

Non-climacteric fruit development and ripening regulation: 'the phytohormones show'

Fruit ripening involves numerous physiological, structural, and metabolic changes that result in the formation of edible fruits. This process is controlled at different molecular levels, with essential roles for phytohormones, transcription factors, and epigenetic modifications. Fleshy fruits are classified as either climacteric or non-climacteric species. Climacteric fruits are characterized by a burst in respiration and ethylene production at the onset of ripening, while regulation of non-climacteric fruit ripening has been commonly attributed to abscisic acid (ABA). However, there is controversy as to whether mechanisms regulating fruit ripening are shared between non-climacteric species, and to what extent other hormones contribute alongside ABA. In this review, we summarize classic and recent studies on the accumulation profile and role of ABA and other important hormones in the regulation of non-climacteric fruit development and ripening, as well as their crosstalk, paying special attention to the two main non-climacteric plant models, strawberry and grape. We highlight both the common and different roles of these regulators in these two crops, and discuss the importance of the transcriptional and environmental regulation of fruit ripening, as well as the need to optimize genetic transformation methodologies to facilitate gene functional analyses.

Transcriptome Analysis Revealed That Hydrogen Peroxide-Regulated Oxidative Phosphorylation Plays an Important Role in the Formation of Pleurotus ostreatus Cap Color

Pleurotus ostreatus is widely cultivated in China. H2O2, as a signaling molecule, can regulate the formation of cap color, but its regulatory pathway is still unclear, severely inhibiting the breeding of dark-colored strains. In this study, 614 DEGs specifically regulated by H2O2 were identified by RNA-seq analysis. GO-enrichment analysis shows that DEGs can be significantly enriched in multiple pathways related to ATP synthesis, mainly including proton-transporting ATP synthesis complex, coupling factor F(o), ATP biosynthetic process, nucleoside triphosphate metabolic processes, ATP metabolic process, purine nucleoside triphosphate biosynthetic and metabolic processes, and purine ribonuclease triphosphate biosynthetic metabolic processes. Further KEGG analysis revealed that 23 DEGs were involved in cap color formation through the oxidative phosphorylation pathway. They were enriched in Complexes I, III, IV, and V in the respiratory chain. Further addition of exogenous uncoupling agents and ATP synthase inhibitors clarifies the important role of ATP synthesis in color formation. In summary, H2O2 may upregulate the expression of complex-encoding genes in the respiratory chain and promote ATP synthesis, thereby affecting the formation of cap color. The results of this study lay the foundation for the breeding of dark-colored strains of P. ostreatus and provide a basis for the color-formation mechanism of edible fungi.

ChIP-Seq Analysis of SlAREB1 Downstream Regulatory Network during Tomato Ripening

SlAREB1, a member of the abscisic acid (ABA) response element-binding factors (AREB/ABFs) family, was reported to play a crucial role in the expression of ABA-regulated downstream genes and affect the ripening of tomato fruit. However, the downstream genes of SlAREB1 are still unclear. Chromatin immunoprecipitation (ChIP) is a powerful tool and a standard method for studying the interactions between DNA and proteins at the genome-wide level. In the present study, SlAREB1 was proved to continually increase until the mature green stage and then decrease during the ripening period, and a total of 972 gene peaks were identified downstream of SlAREB1 by ChIP-seq analysis, mainly located in the intergenic and promoter regions. Further gene ontology (GO) annotation analysis revealed that the target sequence of SlAREB1 was the most involved in biological function. Kyoto Encylopaedia of Genes and Genomes (KEGG) pathway analysis showed that the identified genes were mainly involved in the oxidative phosphorylation and photosynthesis pathways, and some of them were associated with tomato phytohormone synthesis, the cell wall, pigment, and the antioxidant characteristic of the fruit as well. Based on these results, an initial model of SlAREB1 regulation on tomato fruit ripening was constructed, which provided a theoretical basis for further exploring the effects of the regulation mechanism of SlAREB1 and ABA on tomato fruit ripening.

Storage of halved strawberry fruits affects aroma, phytochemical content and gene expression, and is affected by pre-harvest factors

Introduction

Strawberry fruit are highly valued for their aroma which develops during ripening. However, they have a short shelf-life. Low temperature storage is routinely used to extend shelf-life for transport and storage in the supply chain, however cold storage can also affect fruit aroma. Some fruit continue to ripen during chilled storage; however, strawberries are a non-climacteric fruit and hence ripening postharvest is limited. Although most strawberry fruit is sold whole, halved fruit is also used in ready to eat fresh fruit salads which are of increasing consumer demand and pose additional challenges to fresh fruit storage.

Methods

To better understand the effects of cold storage, volatilomic and transcriptomic analyses were applied to halved Fragaria x ananassa cv. Elsanta fruit stored at 4 or 8°C for up to 12 days over two growing seasons.

Results and discussion

The volatile organic compound (VOC) profile differed between 4 or 8°C on most days of storage. Major differences were detected between the two different years of harvest indicating that aroma change at harvest and during storage is highly dependent on environmental factors during growth. The major component of the aroma profile in both years was esters. Over 3000 genes changed in expression over 5 days of storage at 8°C in transcriptome analysis. Overall, phenylpropanoid metabolism, which may also affect VOCs, and starch metabolism were the most significantly affected pathways. Genes involved in autophagy were also differentially expressed. Expression of genes from 43 different transcription factor (TF) families changed in expression: mostly they were down-regulated but NAC and WRKY family genes were mainly up-regulated. Given the high ester representation amongst VOCs, the down-regulation of an alcohol acyl transferase (AAT) during storage is significant. A total of 113 differentially expressed genes were co-regulated with the AAT gene, including seven TFs. These may be potential AAT regulators.

Insights into transcription factors controlling strawberry fruit development and ripening

Fruit ripening is a highly regulated and complex process involving a series of physiological and biochemical changes aiming to maximize fruit organoleptic traits to attract herbivores, maximizing therefore seed dispersal. Furthermore, this process is of key importance for fruit quality and therefore consumer acceptance. In fleshy fruits, ripening involves an alteration in color, in the content of sugars, organic acids and secondary metabolites, such as volatile compounds, which influence flavor and aroma, and the remodeling of cell walls, resulting in the softening of the fruit. The mechanisms underlying these processes rely on the action of phytohormones, transcription factors and epigenetic modifications. Strawberry fruit is considered a model of non-climacteric species, as its ripening is mainly controlled by abscisic acid. Besides the role of phytohormones in the regulation of strawberry fruit ripening, a number of transcription factors have been identified as important regulators of these processes to date. In this review, we present a comprehensive overview of the current knowledge on the role of transcription factors in the regulation of strawberry fruit ripening, as well as in compiling candidate regulators that might play an important role but that have not been functionally studied to date.

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

Fragaria chiloensis (Chilean strawberry) is a native species that produces fruit with an exotic pinkish color and a fruity aroma. It has a non-climacteric pattern of fruit ripening, and it is the mother of the commercial Fragaria x ananassa. The ripening of F. chiloensis fruit seems stimulated by ABA, and a complete set of genes participate in its softening, color, and aroma development. In addition, a set of transcription factors regulate the entire process, but few of them have been described. Over the last two decades, RNA-seq was used to identify genes at three fruit development/ripening stages, named C2 (unripe, large green) to C4 (full ripe), in whole fruit and fruit without achenes. A total of 204,754 contigs were assembled considering all samples, obtaining an N50 of 1.125 bp. Differentially expressed genes (DEGs) between two samples were identified, obtaining a total of 77,181 DEGs. Transcripts for genes involved in ABA biosynthesis present high and differential expression during the C2, C3, and C4 stages. Besides, contigs corresponding to ABA receptors, which interact with a regulatory network, are also differentially expressed. Genes associated with cell wall remodeling and those involved in flavonoid synthesis were also differentially expressed. An interaction network was built considering differentially expressed genes for the phenylpropanoid and flavonoid molecular pathways and having FcMYB1 as a transcription factor regulator. Identifying key genes could give an option to control the ripening of this non-climacteric fruit.

Comparative Transcriptome Analysis of Softening and Ripening-Related Genes in Kiwifruit Cultivars Treated with Ethylene

This work presents the transcriptome analysis of green ‘Hayward’ (Actinidia deliciosa) and gold ‘Haegeum’ (Actinidia chinensis) kiwifruit cultivars after treatment with ethylene for three days at 25 °C. Illumina high-throughput sequencing platform was used to sequence total mRNAs and the transcriptome gene set was constructed by de novo assembly. A total of 1287 and 1724 unigenes were differentially expressed during the comparison of ethylene treatment with control in green ‘Hayward’ and gold ‘Haegeum’, respectively. From the differentially expressed unigenes, 594 and 906 were upregulated, and 693 and 818 were downregulated in the green and gold kiwifruit cultivars, respectively, when treated with ethylene. We also identified a list of genes that were expressed commonly and exclusively in the green and gold kiwifruit cultivars treated with ethylene. Several genes were expressed differentially during the ripening of kiwifruits, and their cumulative effect brought about the softening- and ripening-related changes. This work also identified and categorized genes related to softening and other changes during ripening. Furthermore, the transcript levels of 12 selected representative genes from the differentially expressed genes (DEGs) identified in the transcriptome analysis were confirmed via quantitative real-time PCR (qRT-PCR) to validate the reliability of the expression profiles obtained from RNA-Seq. The data obtained from the present study will add to the information available on the molecular mechanisms of the effects of ethylene during the ripening of kiwifruits. This study will also provide resources for further studies of the genes related to ripening, helping kiwifruit breeders and postharvest technologists to improve ripening quality.

Integrated Metabolomic and Transcriptomic Analysis of the Flavonoid Accumulation in the Leaves of Cyclocarya paliurus at Different Altitudes

Cyclocarya paliurus is a medicinal plant containing flavonoids, triterpenoids, polyphenolics, polysaccharides, and other compounds with diverse biological functions. C. paliurus is distributed across altitudes ranging from 400 to 1,000 m. However, little is known about the effect of altitude on metabolite accumulation in C. paliurus. Also, the biosynthetic pathway involved in flavonoid accumulation in C. paliurus has not been fully elucidated. In this study, mature leaves of C. paliurus growing at low altitude (280 m) and high altitude (920 m) were sampled and subjected to metabolomic and transcriptomic analyses. The flavonoid content and composition were higher in the leaves of C. paliurus collected at high altitude than in those collected at low altitude. Most of the differentially accumulated metabolites (DAMs) were enriched in "flavone and flavonol biosynthesis." The significant differentially expressed genes (DEGs) between low and high altitudes were mainly enriched in "biological process." The most heavily enriched KEGG pathway was related to the subcategory "Oxidative phosphorylation," indicating that complicated biological processes are involved in the response of C. paliurus to harsh environmental factors. High UV-light might be the main influencing factor among the harsh environmental factors found in high altitudes. Integrated analysis of metabolomic and transcriptomic data showed that 31 flavonoids were significantly correlated with 227 DEGs, resulting in 412 related pairs (283 positive and 129 negative) between the DEGs and flavonoids. The possible mechanisms underlying the differentially accumulation of flavonoids at different altitude might be due to variations in transport and relocation of flavonoids in C. paliurus leaves, but not different flavonoid biosynthesis pathways. The up-regulation of genes related to energy and protein synthesis might contribute to flavonoid accumulation at high altitudes. This study broadens our understanding of the effect of altitude on metabolite accumulation and biosynthesis in C. paliurus.

Roles of abscisic acid in regulating ripening and quality of strawberry, a model non-climacteric fruit

Abscisic acid (ABA) is a dominant regulator of ripening and quality in non-climacteric fruits. Strawberry is regarded as a model non-climacteric fruit due to its extensive genetic studies and proven suitability for transgenic approaches to understanding gene function. Strawberry research has contributed to studies on color, flavor development, and fruit softening, and in recent years ABA has been established as a core regulator of strawberry fruit ripening, whereas ethylene plays this role in climacteric fruits. Despite this major difference, several components of the interacting genetic regulatory network in strawberry, such as MADS-box and NAC transcription factors, are similar to those that operate in climacteric fruit. In this review, we summarize recent advances in understanding the role of ABA biosynthesis and signaling and the regulatory network of transcription factors and other phytohormones in strawberry fruit ripening. In addition to providing an update on its ripening, we discuss how strawberry research has helped generate a broader and more comprehensive understanding of the mechanism of non-climacteric fruit ripening and focus attention on the use of strawberry as a model platform for ripening studies.

Roles of abscisic acid in regulating ripening and quality of strawberry, a model non-climacteric fruit

Abscisic acid (ABA) is a dominant regulator of ripening and quality in non-climacteric fruits. Strawberry is regarded as a model non-climacteric fruit due to its extensive genetic studies and proven suitability for transgenic approaches to understanding gene function. Strawberry research has contributed to studies on color, flavor development, and fruit softening, and in recent years ABA has been established as a core regulator of strawberry fruit ripening, whereas ethylene plays this role in climacteric fruits. Despite this major difference, several components of the interacting genetic regulatory network in strawberry, such as MADS-box and NAC transcription factors, are similar to those that operate in climacteric fruit. In this review, we summarize recent advances in understanding the role of ABA biosynthesis and signaling and the regulatory network of transcription factors and other phytohormones in strawberry fruit ripening. In addition to providing an update on its ripening, we discuss how strawberry research has helped generate a broader and more comprehensive understanding of the mechanism of non-climacteric fruit ripening and focus attention on the use of strawberry as a model platform for ripening studies.

Comprehensive genome-wide analysis of calmodulin-binding transcription activator (CAMTA) in Durio zibethinus and identification of fruit ripening-associated DzCAMTAs

Background

Fruit ripening is an intricate developmental process driven by a highly coordinated action of complex hormonal networks. Ethylene is considered as the main phytohormone that regulates the ripening of climacteric fruits. Concomitantly, several ethylene-responsive transcription factors (TFs) are pivotal components of the regulatory network underlying fruit ripening. Calmodulin-binding transcription activator (CAMTA) is one such ethylene-induced TF implicated in various stress and plant developmental processes.

Results

Our comprehensive analysis of the CAMTA gene family in Durio zibethinus (durian, Dz) identified 10 CAMTAs with conserved domains. Phylogenetic analysis of DzCAMTAs, positioned DzCAMTA3 with its tomato ortholog that has already been validated for its role in the fruit ripening process through ethylene-mediated signaling. Furthermore, the transcriptome-wide analysis revealed DzCAMTA3 and DzCAMTA8 as the highest expressing durian CAMTA genes. These two DzCAMTAs possessed a distinct ripening-associated expression pattern during post-harvest ripening in Monthong, a durian cultivar native to Thailand. The expression profiling of DzCAMTA3 and DzCAMTA8 under natural ripening conditions and ethylene-induced/delayed ripening conditions substantiated their roles as ethylene-induced transcriptional activators of ripening. Similarly, auxin-suppressed expression of DzCAMTA3 and DzCAMTA8 confirmed their responsiveness to exogenous auxin treatment in a time-dependent manner. Accordingly, we propose that DzCAMTA3 and DzCAMTA8 synergistically crosstalk with ethylene during durian fruit ripening. In contrast, DzCAMTA3 and DzCAMTA8 antagonistically with auxin could affect the post-harvest ripening process in durian. Furthermore, DzCAMTA3 and DzCAMTA8 interacting genes contain significant CAMTA recognition motifs and regulated several pivotal fruit-ripening-associated pathways.

Conclusion

Taken together, the present study contributes to an in-depth understanding of the structure and probable function of CAMTA genes in the post-harvest ripening of durian.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08022-1.

The NAC transcription factor FaRIF controls fruit ripening in strawberry

In contrast to climacteric fruits such as tomato, the knowledge on key regulatory genes controlling the ripening of strawberry, a nonclimacteric fruit, is still limited. NAC transcription factors (TFs) mediate different developmental processes in plants. Here, we identified and characterized Ripening Inducing Factor (FaRIF), a NAC TF that is highly expressed and induced in strawberry receptacles during ripening. Functional analyses based on stable transgenic lines aimed at silencing FaRIF by RNA interference, either from a constitutive promoter or the ripe receptacle-specific EXP2 promoter, as well as overexpression lines showed that FaRIF controls critical ripening-related processes such as fruit softening and pigment and sugar accumulation. Physiological, metabolome, and transcriptome analyses of receptacles of FaRIF-silenced and overexpression lines point to FaRIF as a key regulator of strawberry fruit ripening from early developmental stages, controlling abscisic acid biosynthesis and signaling, cell-wall degradation, and modification, the phenylpropanoid pathway, volatiles production, and the balance of the aerobic/anaerobic metabolism. FaRIF is therefore a target to be modified/edited to control the quality of strawberry fruits.

Expanded transcriptomic view of strawberry fruit ripening through meta-analysis

Strawberry is an important fruit crop and a model for studying non-climacteric fruit ripening. Fruit ripening and senescence influence strawberry fruit quality and postharvest storability, and have been intensively studied. However, genetic and physiological differences among cultivars preclude consensus understanding of these processes. We therefore performed a meta-analysis by mapping existing transcriptome data to the newly published and improved strawberry reference genome and extracted meta-differentially expressed genes (meta-DEGs) from six cultivars to provide an expanded transcriptomic view of strawberry ripening. We identified cultivar-specific transcriptome changes in anthocyanin biosynthesis-related genes and common changes in cell wall degradation, chlorophyll degradation, and starch metabolism-related genes during ripening. We also identified 483 meta-DEGs enriched in gene ontology categories related to photosynthesis and amino acid and fatty acid biosynthesis that had not been revealed in previous studies. We conclude that meta-analysis of existing transcriptome studies can effectively address fundamental questions in plant sciences.

Grapevine U-Box E3 Ubiquitin Ligase VlPUB38 Negatively Regulates Fruit Ripening by Facilitating Abscisic-Aldehyde Oxidase Degradation

The plant U-box E3 ubiquitin ligase-mediated ubiquitin/26S proteasome degradation system plays a key role in plant growth and development. Previously identified as a member of the grape PUB gene family, PUB38 was shown to participate in the berry-ripening progress. Here, we demonstrate that the E3 ligase VlPUB38 mediates abscisic acid (ABA) synthesis via 26S proteasome degradation and its involvement in regulating fruit-ripening processes. Strawberry-overexpressing VlPUB38 lines displayed obvious inhibition of mature phenotype, and this was rescued by exogenous ABA treatment and MG132. Post-ABA treatment, expression levels of ABA response-related genes in VlPUB38-overexpressed Arabidopsis significantly exceeded controls. Strawberry and Arabidopsis ectopic expression assays suggest that VlPUB38 negatively regulates fruit ripening in an ABA-dependent manner. Moreover, VlPUB38 has ubiquitin ligase activity, which depends on the U-box-conserved domain. VlPUB38 interacts with abscisic-aldehyde oxidase (VlAAO), targeting VlAAO proteolysis via the 26S proteasome system. These results indicate that VlPUB38 negatively regulates grape fruit ripening by mediating the degradation of key factor VlAAO in the ABA synthesis pathway.

Genome-wide identification of ubiquitin proteasome subunits as superior reference genes for transcript normalization during receptacle development in strawberry cultivars

Background

Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars.

Results

The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the “Commonly used” and “Traditional” HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development.

Conclusion

These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07393-9.

Proteomic Changes in Antioxidant System in Strawberry During Ripening

To investigate the strawberry antioxidant defense system during fruit ripening, a targeted quantitative proteomic approach using multiple reaction monitoring (MRM) was developed to investigate targeted proteins in the antioxidant enzyme system in strawberry fruit. We investigated 46 proteins and isoforms with 73 identified peptides which may be involved in this antioxidant enzyme system. Among the proteins that changed during ripening, aldo/keto reductase (AKR), superoxide dismutase (SOD) and glutathione transferase (GT) increased significantly, while dehydroascorbate reductase, 2-Cys peroxiredoxin, catalase (CAT), 1-Cys peroxiredoxin and L-ascorbate peroxidase (APX) decreased significantly. These results suggest that fruit ripening of strawberry activates the enzymes of an SOD/glutathione metabolism system. The methodologies used in this study will be useful for systematically characterizing the role of antioxidant enzymes in fruit ripening of other plants.

Genome-wide interologous interactome map (TeaGPIN) of Camellia sinensis

Tea, prepared from the young leaves of Camellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1302 key proteins are reported in tea to have p-value <0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.

Sugar Signaling During Fruit Ripening

Sugars play a key role in fruit quality, as they directly influence taste, and thus consumer acceptance. Carbohydrates are the main resources needed by the plant for carbon and energy supply and have been suggested to be involved in all the important developmental processes, including embryogenesis, seed germination, stress responses, and vegetative and reproductive growth. Recently, considerable progresses have been made in understanding regulation of fruit ripening mechanisms, based on the role of ethylene, auxins, abscisic acid, gibberellins, or jasmonic acid, in both climacteric and non-climacteric fruits. However, the role of sugar and its associated molecular network with hormones in the control of fruit development and ripening is still poorly understood. In this review, we focus on sugar signaling mechanisms described up to date in fruits, describing their involvement in ripening-associated processes, such as pigments accumulation, and their association with hormone transduction pathways, as well as their role in stress-related responses.

A Clathrin-Related Protein, SCD2/RRP1, Participates in Abscisic Acid Signaling in Arabidopsis

Abscisic acid (ABA) plays important roles in many aspects of plant growth and development, and responses to diverse stresses. Although much progress has been made in understanding the molecular mechanisms of ABA homoeostasis and signaling, the mechanism by which plant cells integrate ABA trafficking and signaling to regulate plant developmental processes is poorly understood. In this study, we used Arabidopsis STOMATAL CYTOKINESIS DEFECTIVE 2/RIPENING-REGULATED PROTEIN 1 (SCD2/RRP1) mutants and overexpression plants, in combination with transcriptome and protein-interaction assays, to investigate SCD2/RRP1 involvement in the integration of ABA trafficking and signaling in seed germination and seedling growth. Manipulation of SCD2/RRP1 expression affected ABA sensitivity in seed germination and seedling growth, as well as transcription of several ABA transporter genes and ABA content. RNA-sequencing analysis of Arabidopsis transgenic mutants suggested that SCD2/RRP1 was associated with ABA signaling via a type 2C protein phosphatase (PP2C) protein. The N- and C-terminal regions of SCD2/RRP1 separately interacted with both PYRABACTIN RESISTANCE 1 (PYR1) and ABA INSENSITIVE 1 (ABI1) on the plasma membrane, and SCD2/RRP1 acted genetically upstream of ABI1. Interestingly, ABA inhibited the interaction of SCD2/RRP1 with ABI1, but did not affect the interaction of SCD2/RRP1 with PYR1. These results suggested that in Arabidopsis SCD2/RRP1participates in early seed development and growth potentially through clathrin-mediated endocytosis- and clathrin-coated vesicle-mediated ABA trafficking and signaling. These findings provide insight into the mechanism by which cells regulate plant developmental processes through ABA.

1-Methylcyclopropene treatment controls ethanol accumulation associated with regulation of mitochondrial energy metabolism in kiwifruit (Actinidia deliciosa) cv. "Bruno" during storage at room temperature

In this paper, the effects of 1-methylcyclopropene (1-MCP) treatment on the ethanol accumulation and mitochondrial energy metabolism in kiwifruit (Actinidia deliciosa) cv. "Bruno" were investigated during storage at room temperature (24 ± 1°C). The results showed that 1-MCP treatment significantly reduced the ethanol accumulation, maintained higher levels of adenosine triphosphate (ATP) content and energy charge (EC), enhanced enzymes activities involved in mitochondrial energy metabolism, such as succinic dehydrogenase, cytochrome C oxidase, H⁺ -adenosine triphosphatase (H⁺ -ATPase), and Ca²⁺ -adenosine triphosphatase (Ca²⁺ -ATPase), and regulated the NADH/NAD⁺ ratio, and pyruvate to tricarboxylic acid cycle (TCA) by suppressing the glutamate-pyruvate transaminase and promoting the pyruvate dehydrogenase activity, and decarboxylation of citric acid in harvested kiwifruit. These shifts in mitochondrial energy metabolism and oxidative phosphorylation correlated the higher ATP yield and an elevated EC with lower ethanol accumulation (13.71% of those in the control fruit) under 1-MCP treatment, and reduced the susceptibility of ethanol related off-flavor disorder in kiwifruit during storage. PRACTICAL APPLICATIONS: A kiwifruit (Actinidia deliciosa) cv. "Bruno," a major cultivated kiwifruit in China, is prone to accumulate ethanol sharply after respiratory climacteric during storage. Ethanol has been accounted as a vital aroma volatile metabolite in various fruits. However, over accumulation of ethanol often leads to the development of alcohol off-flavor disorder, particularly in typical climacteric fruit such as kiwifruit. This work was aimed to maintain the flavor quality of kiwifruit cv. "Bruno" via improving the mitochondrial energy metabolism and functional TCA cycle, and limiting the ethanol accumulation under 1-MCP treatment. Thus, 1-MCP treatment could be beneficial to prevent the occurrence of alcohol off-flavor disorder along with sustainment of the flavor quality of kiwifruit cv. "Bruno" during storage at room temperature.

Cytosolic/Plastid Glyceraldehyde-3-Phosphate Dehydrogenase Is a Negative Regulator of Strawberry Fruit Ripening

Cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) and plastid glyceraldehyde-3-phosphate dehydrogenase (GAPCp) are key enzymes in glycolysis. Besides their catalytic function, GAPC/GAPCp participates in the regulation of plant stress response and growth and development. However, the involvement of GAPC/GAPCp in the regulation of fruit ripening is unclear. In this study, FaGAPC2 and FaGAPCp1 in strawberries were isolated and analyzed. FaGAPC2 and FaGAPCp1 transcripts showed high transcript levels in the fruit. Transient overexpression of FaGAPC2 and FaGAPCp1 delayed fruit ripening, whereas RNA interference promoted fruit ripening and affected fruit anthocyanins and sucrose levels. Change in the expression patterns of FaGAPC2 and FaGAPCp1 also influenced the expression of several glycolysis-related and ripening-related genes such as CEL1, CEL2, SS, ANS, MYB5, NCED1, ABI1, ALDO, PK, and G6PDH, and H₂O₂ level and reduced glutathione (GSH)/glutathione disulfide (GSSG) redox potential. Meanwhile, metabolomics experiments showed that transient overexpression of FaGAPCp1 resulted in a decrease in anthocyanins, flavonoids, organic acid, amino acids, and their derivatives. In addition, abscisic acid (ABA) and sucrose treatment induced the production of large amounts of H₂O₂ and inhibited the expression of FaGAPC2/FaGAPCp1 in strawberry fruit. These results revealed that FaGAPC2/FaGAPCp1 is a negative regulator of ABA and sucrose mediated fruit ripening which can be regulated by oxidative stress.

FaPAO5 regulates Spm/Spd levels as a signaling during strawberry fruit ripening

Polyamines are important for non-climacteric fruit ripening according to an analysis of the model plant strawberry. However, the molecular mechanism underlying the polyamine accumulation during ripening has not been fully elucidated. In this study, an examination of our proteome data related to strawberry fruit ripening revealed a putative polyamine oxidase 5, FaPAO5, which was localized in the cytoplasm and nucleus. Additionally, FaPAO5 expression levels as well as the abundance of the encoded protein continually decreased during ripening. Inhibiting FaPAO5 expression by RNAi promoted Spd, Spm, and ABA accumulation while inhibited H2O2 production, which ultimately enhanced ripening as evidenced by the ripening-related events and corresponding gene expression changes. The opposite effects were observed in FaPAO5-overexpressing transgenic fruits. Analyses of the binding affinity and enzymatic activity of FaPAO5 with Spm, Spd, and Put uncovered a special role for FaPAO5 in the terminal catabolism of Spm and Spd, with a K d of 0.21 and 0.29 µM, respectively. Moreover, FaPAO5 expression was inhibited by ABA and promoted by Spd and Spm. Furthermore, the RNA-seq analysis of RNAi and control fruits via differentially expressed genes (DEGs) indicated the six most enriched pathways among the differentially expressed genes were related to sugar, abscisic acid, ethylene, auxin, gibberellin, and Ca2+. Among four putative PAO genes in the strawberry genome, only FaPAO5 was confirmed to influence fruit ripening. In conclusion, FaPAO5 is a negative regulator of strawberry fruit ripening and modulates Spm/Spd levels as a signaling event, in which ABA plays a central role.

Proteomic and metabolic analysis reveals novel sweet cherry fruit development regulatory points influenced by girdling

Despite the application of girdling technique for several centuries, its impact on the metabolic shifts that underly fruit biology remains fragmentary. To characterize the influence of girdling on sweet cherry (Prunus avium L.) fruit development and ripening, second-year-old shoots of the cultivars 'Lapins' and 'Skeena' were girdled before full blossom. Fruit characteristics were evaluated across six developmental stages (S), from green-small fruit (stage S1) to full ripe stage (stage S6). In both cultivars, girdling significantly altered the fruit ripening physiognomy. Time course fruit metabolomic along with proteomic approaches unraveled common and cultivar-specific responses to girdling. Notably, several primary and secondary metabolites, such as soluble sugars (glucose, trehalose), alcohol (mannitol), phenolic compounds (rutin, naringenin-7-O-glucoside), including anthocyanins (cyanidin-3-O-rutinoside, cyanidin-3-O-galactoside, cyanidin-3.5-O-diglucoside) were accumulated by girdling, while various amino acids (glycine, threonine, asparagine) were decreased in both cultivars. Proteins predominantly associated with ribosome, DNA repair and recombination, chromosome, membrane trafficking, RNA transport, oxidative phosphorylation, and redox homeostasis were depressed in fruits of both girdled cultivars. This study provides the first system-wide datasets concerning metabolomic and proteomic changes in girdled fruits, which reveal that shoot girdling may induce long-term changes in sweet cherry metabolism.

Transcriptome profiling of non-climacteric 'yellow' melon during ripening: insights on sugar metabolism

BACKGROUND

The non-climacteric 'Yellow' melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related pathways can contribute to the development of new field management and post-harvest practices, making it possible to deliver better quality fruits to consumers.

RESULTS

The RNA-seq associated with RT-qPCR analyses of four maturation stages were performed to identify important enzymes and pathways that are involved in the ripening profile of non-climacteric 'Yellow' melon fruit focusing on sugar metabolism. We identified 895 genes 10 days after pollination (DAP)-biased and 909 genes 40 DAP-biased. The KEGG pathway enrichment analysis of these differentially expressed (DE) genes revealed that 'hormone signal transduction', 'carbon metabolism', 'sucrose metabolism', 'protein processing in endoplasmic reticulum' and 'spliceosome' were the most differentially regulated processes occurring during melon development. In the sucrose metabolism, five DE genes are up-regulated and 12 are down-regulated during fruit ripening.

CONCLUSIONS

The results demonstrated important enzymes in the sugar pathway that are responsible for the sucrose content and maturation profile in non-climacteric 'Yellow' melon. New DE genes were first detected for melon in this study such as invertase inhibitor LIKE 3 (CmINH3), trehalose phosphate phosphatase (CmTPP1) and trehalose phosphate synthases (CmTPS5, CmTPS7, CmTPS9). Furthermore, the results of the protein-protein network interaction demonstrated general characteristics of the transcriptome of young and full-ripe melon and provide new perspectives for the understanding of ripening.

The Physiological and Molecular Mechanism of Abscisic Acid in Regulation of Fleshy Fruit Ripening

The ripening of fleshy fruits is coupled with the degradation of both chlorophyll and cell walls, as well as changes in the metabolism of phenylpropanoids, flavonoids, starch/sucrose, and carotenoids. These processes are controlled by phytohormones and other factors, including abscisic acid (ABA), ethylene, auxin, polyamines, sugar, and reactive oxygen species. The ripening of climacteric fruits is controlled by ethylene and non-climacteric fruit ripening is regulated mainly by ABA. Also, ABA and ethylene may interact in both types of fruit ripening. ABA concentrations in fleshy fruits are regulated in response to developmental and environmental cues and are controlled by the relative rates of ABA biosynthesis and catabolism, the former mainly via 9-cis-epoxycarotenoid dioxygenases (NCEDs) and β-glucosidases and the latter via ABA 8'-hydroxylases (CYP707As) and β-glycosyltransferases. In strawberry fruit ripening, ABA is perceived via at least two receptors, Pyrabactin resistance (PYR)/PYR-like (PYL) and putative abscisic acid receptor (ABAR), which are linked separately to the conserved signaling pathway ABA-FaPYR1-FaABIl-FaSnRK2 and the novel signaling pathway ABA-FaABAR-FaRIPK1-FaABI4. Downstream signaling components include important transcription factors, such as AREB (ABA responsive element binding protein)/ABF (ABRE binding factors ABA responsive factor), ethylene response factor (ERF), and V-myb Myeloblastosis viral oncogene homolog (MYB), as well as ripening-related genes. Finally, a comprehensive model of ABA linked to ethylene, sugar, polyamines, auxin and reactive oxygen species in the regulation of strawberry fruit ripening is proposed. Next, new integrated mechanisms, including two ABA signaling pathways, ABA and ethylene signaling pathways, and ABA/ethylene to other phytohormones are interesting and important research topics in ripening, especially in non-climacteric fruits.

ABA and sucrose co-regulate strawberry fruit ripening and show inhibition of glycolysis

Abscisic acid (ABA) and sucrose play an important role in strawberry fruit ripening, but how ABA and sucrose co-regulate this ripening progress remains unclear. The intention of this study was to examine the effect of ABA and sucrose on strawberry fruit ripening and to evaluate the ABA/sucrose interaction mechanism on the strawberry fruit ripening process. Here, we report that there is an acute synergistic effect between ABA and sucrose in accelerating strawberry fruit ripening. The time frame of fruit development and ripening was shortened after the application of ABA, sucrose, and ABA + sucrose, but most of the major quality parameters in treated-ripe fruit, including fruit weight, total soluble solids, anthocyanin, ascorbic acid, the total phenolic content, lightness (L*), chroma (C*), and hue angle (h°) values were not affected. Meanwhile, the endogenous ABA and sucrose levels, and the expression of ABA and sucrose signaling genes and ripening-related genes, such as NCED1, NCED2, SnRK2.2, SuSy, MYB5, CEL1, and CEL2, was all significantly enhanced by ABA or sucrose treatment alone, but in particular, by the ABA + sucrose treatment. Therefore, improving the ripening regulation efficiency is one synergetic action of ABA/sucrose. Another synergetic action of ABA/sucrose shows that a short inhibition of glycolysis occurs during accelerated strawberry ripening. ABA and sucrose can induce higher accumulation of H₂O₂, leading to a transient decrease in glycolysis. Conversely, lower endogenous H₂O₂ levels caused by reduced glutathione (GSH) treatment resulted in a transient increase in glycolysis while delaying strawberry fruit ripening. Collectively, this study demonstrates that the ABA/sucrose interaction affects the ripening regulation efficiency and shows inhibition of glycolysis.

An integrated metabolomic and gene expression analysis identifies heat and calcium metabolic networks underlying postharvest sweet cherry fruit senescence

Ηeat and calcium treatments reprogram sweet cherry fruit metabolism during postharvest senescence as evidenced by changes in respiration, amino acid metabolism, sugars, and secondary metabolites shift. Heat and calcium treatments are used to improve postharvest fruit longevity; however, the exact mechanism remains poorly understood. To characterize the impact of these treatments on sweet cherries metabolism, 'Lapins' fruits were treated with heat or CaCl₂ solutions and their combination and subsequently were exposed at room temperature, for up to 4 days, defined as senescence period. Single and combined heat and calcium treatments partially delayed fruit senescence, as evidenced by changes in fruit colour darkening, skin penetration force, and respiration activity. Calcium content was noticeably increased by heat in Ca-treated fruit. Several primary metabolites, including amino acids, organic acids, and alcohols, were decreased in response to both treatments, while many soluble sugars and secondary metabolites were increased within 1 day post-treatment. Changes of several metabolites in heat-treated fruits, especially esculetin, peonidin 3-O-glucoside and peonidin 3-O-galactoside, ribose, pyroglutamate, and isorhamnetin-3-O-rutinoside, were detected. The metabolome of fruit exposed to calcium also displayed substantial modulations, particularly in the levels of galactose, glycerate, aspartate, tryptophan, phospharate rutin, and peonidin 3-O-glucoside. The expression of several genes involved in TCA cycle (MDH1, IDH1, OGDH, SUCLA2, and SDH1-1), pectin degradation (ADPG1) as well as secondary (SK1, 4CL1, HCT, and BAN), amino acids (ALDH18A1, ALDH4A1, GS, GAD, GOT2, OPLAH, HSDH, and SDS), and sugar (PDHA1 and DLAT) metabolism were affected by both treatments. Pathway-specific analysis further revealed the regulation of fruit metabolic programming by heat and calcium. This work provides a comprehensive understanding of metabolic regulation in response to heat and calcium during fruit senescence.

Sucrose Promotes Strawberry Fruit Ripening and Affects Ripening-Related Processes

Strawberry is a typical nonclimacteric fruit, whose ripening mechanism needs to be further investigated. Sucrose has been recently proved as a signal molecule, participating in strawberry fruit ripening and related processes. While in the effects of sucrose application timing and concentration on ripening, fruit qualities remain unclear, as well as the transcriptome-wide details about the effects of sucrose on the gene expression involved in ripening-related processes. In this study, strawberry fruits at the degreening (DG), white (W), and initial-red (IR) stages were treated with different concentration of sucrose. The results showed that anthocyanin was increased while total polyphenol concentration (TPC) and total flavonoid concentration (TFC) were decreased during fruit development after sucrose treatment. Interestingly, It was showed that 100 mM sucrose application at the DG stage had the most obvious effects on fruit ripening; it made all the fruits turn into full-red (FR) around 4 days (d) earlier than the control, while it did not affect fruit quality traits and most bioactive compounds in the FR fruits. Subsequently, RNA sequencing (RNAseq) of the fruits collected at 8 days after 100 mM sucrose treatment was carried out. It was suggested that 993 genes were differentially expressed comparing with the control. Transcriptome-based expression analysis revealed that sucrose induced the expression of genes involved in the AsA and anthocyanin biosynthesis, while largely suppressed the expression of genes in TCA. The results obtained in this study provided more expression profiles of ripening-related genes under the treatment of sucrose, which will contribute to a better understanding for the mechanism underlying sucrose-induced fruit ripening.

The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis

Apricots, scientifically known as Prunus armeniaca L, are drupes that resemble and are closely related to peaches or plums. As one of the top consumed fruits, apricots are widely grown worldwide except in Antarctica. A high-quality reference genome for apricot is still unavailable, which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background, evolutionary diversity, and population diversity in apricot. DNA from P. armeniaca was used to generate a standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on Sequel SMRT Cells, generating a total of 16.54 Gb of PacBio subreads (N50 = 13.55 kb). The high-quality P. armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70× coverage and 171× Illumina reads (40.46 Gb), combined with a genetic map for chromosome scaffolding. The assembled genome size was 221.9 Mb, with a contig NG50 size of 1.02 Mb. Scaffolds covering 92.88% of the assembled genome were anchored on eight chromosomes. Benchmarking Universal Single-Copy Orthologs analysis showed 98.0% complete genes. We predicted 30,436 protein-coding genes, and 38.28% of the genome was predicted to be repetitive. We found 981 contracted gene families, 1324 expanded gene families and 2300 apricot-specific genes. The differentially expressed gene (DEG) analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase (NCED) gene but not lycopene beta-cyclase (LcyB) gene results in a low β-carotenoid content in the white cultivar "Dabaixing". This complete and highly contiguous P. armeniaca reference genome will be of help for future studies of resistance to plum pox virus (PPV) and the identification and characterization of important agronomic genes and breeding strategies in apricot.

Transcriptome profiling of 'Kyoho' grape at different stages of berry development following 5-azaC treatment

Background

5-Azacytidine (5-azaC) promotes the development of ‘Kyoho’ grape berry but the associated changes in gene expression have not been reported. In this study, we performed transcriptome analysis of grape berry at five developmental stages after 5-azaC treatment to elucidate the gene expression networks controlling berry ripening.

Results

The expression patterns of most genes across the time series were similar between the 5-azaC treatment and control groups. The number of differentially expressed genes (DEGs) at a given developmental stage ranged from 9 (A3_C3) to 690 (A5_C5). The results indicated that 5-azaC treatment had not very great influences on the expressions of most genes. Functional annotation of the DEGs revealed that they were mainly related to fruit softening, photosynthesis, protein phosphorylation, and heat stress. Eight modules showed high correlation with specific developmental stages and hub genes such as PEROXIDASE 4, CAFFEIC ACID 3-O-METHYLTRANSFERASE 1, and HISTONE-LYSINE N-METHYLTRANSFERASE EZA1 were identified by weighted gene correlation network analysis.

Conclusions

5-AzaC treatment alters the transcriptional profile of grape berry at different stages of development, which may involve changes in DNA methylation.

Strawberry tonoplast transporter, FaVPT1, controls phosphate accumulation and fruit quality

Phosphorus (P) is essential for plant growth and development, and the vacuole is an important organelle for phosphate storage. However, the tonoplast phosphate transporter in fleshy fruits remains unknown. In this study, based on the strawberry (Fragaria × ananassa) fruit transcriptome data, a tonoplast-localized vacuolar phosphate transporter with SPX and major facilitator superfamily domains, FaVPT1, was identified. FaVPT1 expression was highest in the fruits and could be induced by sucrose. Using transient transgenic systems in strawberry fruit, the downregulation and upregulation of FaVPT1 inhibited and promoted ripening, respectively, and affected phosphate contents, fruit firmness, sugar and anthocyanin contents, and ripening-related gene transcription. FaVPT1 could rescue Pi absorption in both yeast and the Arabidopsis atvpt1 mutant, confirming the similar function of FaVPT1 and AtVPT1, a previously identified tonoplast phosphate transporter in Arabidopsis. The Escherichia coli-expressed SPX domain of FaVPT1 could strongly bind to InsP₆ with a K_d of 3.5 μM. The results demonstrate that FaVPT1 is a tonoplast phosphate transporter and regulates strawberry fruit ripening and quality, to a large extent, via sucrose.

Transcriptome analysis provides insights into the stress response crosstalk in apple (Malus × domestica) subjected to drought, cold and high salinity

Drought, cold, and high salinity are three major abiotic stresses effecting apple tree growth and fruit production. Understanding the genetic mechanisms of crosstalk between stress responses signalling networks and identifying the genes involved in apple has potential importance for crop improvement and breeding strategies. Here, the transcriptome profiling analysis of in vitro-grown apple plants subjected to drought, cold and high salinity stress, showed a total of 377 upregulated and 211 downregulated common differentially expressed genes (DEGs) to all 3 stress treatments compared with the control. Gene Ontology (GO) analysis indicated that these common DEGs were enriched in ‘metabolic process’ under the ‘biological process’ category, as well as in ‘binding’ and ‘catalytic activity’ under the ‘molecular function’ category. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that common DEGs were mainly belong to the ‘biological functions’ category and 17 DEGs were identified in ‘environmental information processing’ sub-category which may act as signal transduction components in response crosstalk regulation. Overexpression of 5 upregulated genes individually, out of these 17 common DEGs in apple calli promoted the consistent upregulation of DREB6, CBF1 and ZAT10 and increased the mass weight and antioxidase ability, implying these five common DEGs involved in multiple pathways and improved comprehensive resistance to stress.

Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea

The fungal pathogen Botrytis cinerea causes grey mould, a commercially damaging disease of strawberry. This pathogen affects fruit in the field, storage, transport and market. The presence of grey mould is the most common reason for fruit rejection by growers, shippers and consumers, leading to significant economic losses. Here, we review the biology and epidemiology of the pathogen, mechanisms of infection and the genetics of host plant resistance. The development of grey mould is affected by environmental and genetic factors; however, little is known about how B. cinerea and strawberry interact at the molecular level. Despite intensive efforts, breeding strawberry for resistance to grey mould has not been successful, and the mechanisms underlying tolerance to B. cinerea are poorly understood and under-investigated. Current control strategies against grey mould include pre- and postharvest fungicides, yet they are generally ineffective and expensive. In this review, we examine available research on horticultural management, chemical and biological control of the pathogen in the field and postharvest storage, and discuss their relevance for integrative disease management. Additionally, we identify and propose approaches for increasing resistance to B. cinerea in strawberry by tapping into natural genetic variation and manipulating host factors via genetic engineering and genome editing.

Virus-induced gene silencing: empowering genetics in non-model organisms

Virus-induced gene silencing (VIGS) is an RNA interference-based technology used to transiently knock down target gene expression by utilizing modified plant viral genomes. VIGS can be adapted to many angiosperm species that cover large phylogenetic distances, allowing the analysis of gene functions in species that are not amenable to stable genetic transformation. With a vast amount of sequence information already available and even more likely to become available in the future, VIGS provides a means to analyze the functions of candidate genes identified in large genomic or transcriptomic screens. Here, we provide a comprehensive overview of target species and VIGS vector systems, assess recent key publications in the field, and explain how plant viruses are modified to serve as VIGS vectors. As many reports on the VIGS technique are being published, we also propose minimal reporting guidelines for carrying out these experiments, with the aim of increasing comparability between experiments. Finally, we propose methods for the statistical evaluation of phenotypic results obtained with VIGS-treated plants, as analysis is challenging due to the predominantly transient nature of the silencing effect.

Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla

To investigate the molecular mechanism underlying fruit development and color change, comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages (green fruit stage, turning stage, and ripe fruit stage). We identified 25,699 long noncoding RNAs (lncRNAs) derived from 25,107 loci in the F. pentaphylla fruit transcriptome, which showed distinct stage- and genotype-specific expression patterns. Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F. pentaphylla varieties. The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis, suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F. pentaphylla. Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total. Functional annotation of target genes suggested that lncRNAs in F. pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors. Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F. pentaphylla.

MicroRNA profiling analysis of developing berries for 'Kyoho' and its early-ripening mutant during berry ripening

BACKGROUND

'Fengzao' is an early-ripening bud mutant of 'Kyoho', which matures nearly 30 days earlier than 'Kyoho'. To gain a better understanding of the regulatory role of miRNAs in early-ripening of grape berry, high-throughput sequencing approach and quantitative RT-PCR validation were employed to identify miRNAs at the genome-wide level and profile the expression patterns of the miRNAs during berry development in 'Kyho' and 'Fengzao', respectively.

RESULTS

Nine independent small RNA libraries were constructed and sequenced in two varieties from key berry development stages. A total of 108 known miRNAs and 61 novel miRNAs were identified. Among that, 159 miRNAs identified in 'Fengzao' all completely expressed in 'Kyoho' and there were 10 miRNAs specifically expressed in 'Kyoho'. The expression profiles of known and novel miRNAs were quite similar between two varieties. As the major differentially expressed miRNAs, novel_144, vvi-miR3626-3p and vvi-miR3626-5p only expressed in 'Kyoho', vvi-miR399b and vvi-miR399e were down-regulated in 'Fengzao', while vvi-miR477b-3p up-regulated in 'Fengzao'. According to the expression analysis and previous reports, miR169-NF-Y subunit, miR398-CSD, miR3626-RNA helicase, miR399- phosphate transporter and miR477-GRAS transcription factor were selected as the candidates for further investigations of miRNA regulation role in the early-ripening of grape. The qRT-PCR analyses validated the contrasting expression patterns for these miRNAs and their target genes.

CONCLUSIONS

The miRNAome of the grape berry development of 'Kyoho', and its early-ripening bud mutant, 'Fengzao' were compared by high-throughput sequencing. The expression pattern of several key miRNAs and their target genes during grape berry development and ripening stages was examined. Our results provide valuable basis towards understanding the regulatory mechanisms of early-ripening of grape berry.

Characterization of the hot pepper (Capsicum frutescens) fruit ripening regulated by ethylene and ABA

BACKGROUND

Ripening of fleshy fruits has been classically defined as climacteric or non-climacteric. Both types of ripening are controlled by plant hormones, notably by ethylene in climacteric ripening and by abscisic acid (ABA) in non-climacteric ripening. In pepper (Capsicum), fruit ripening has been widely classified as non-climacteric, but the ripening of the hot pepper fruit appears to be climacteric. To date, how to regulate the hot pepper fruit ripening through ethylene and ABA remains unclear.

RESULTS

Here, we examined ripening of the hot pepper (Capsicum frutescens) fruit during large green (LG), initial colouring (IC), brown (Br), and full red (FR) stages. We found a peak of ethylene emission at the IC stage, followed by a peak respiratory quotient at the Br stage. By contrast, ABA levels increased slowly before the Br stage, then increased sharply and reached a maximum level at the FR stage. Exogenous ethylene promoted colouration, but exogenous ABA did not. Unexpectedly, fluridone, an inhibitor of ABA biosynthesis, promoted colouration. RNA-sequencing data obtained from the four stages around ripening showed that ACO3 and NCED1/3 gene expression determined ethylene and ABA levels, respectively. Downregulation of ACO3 and NCED1/3 expression by virus-induced gene silencing (VIGS) inhibited and promoted colouration, respectively, as evidenced by changes in carotenoid, ABA, and ethylene levels, as well as carotenoid biosynthesis-related gene expression. Importantly, the retarded colouration in ACO3-VIGS fruits was rescued by exogenous ethylene.

CONCLUSIONS

Ethylene positively regulates the hot pepper fruit colouration, while inhibition of ABA biosynthesis promotes colouration, suggesting a role of ABA in de-greening. Our findings provide new insights into processes of fleshy fruit ripening regulated by ABA and ethylene, focusing on ethylene in carotenoid biosynthesis and ABA in chlorophyll degradation.

Characterization of the hot pepper (Capsicum frutescens) fruit ripening regulated by ethylene and ABA

BACKGROUND

Ripening of fleshy fruits has been classically defined as climacteric or non-climacteric. Both types of ripening are controlled by plant hormones, notably by ethylene in climacteric ripening and by abscisic acid (ABA) in non-climacteric ripening. In pepper (Capsicum), fruit ripening has been widely classified as non-climacteric, but the ripening of the hot pepper fruit appears to be climacteric. To date, how to regulate the hot pepper fruit ripening through ethylene and ABA remains unclear.

RESULTS

Here, we examined ripening of the hot pepper (Capsicum frutescens) fruit during large green (LG), initial colouring (IC), brown (Br), and full red (FR) stages. We found a peak of ethylene emission at the IC stage, followed by a peak respiratory quotient at the Br stage. By contrast, ABA levels increased slowly before the Br stage, then increased sharply and reached a maximum level at the FR stage. Exogenous ethylene promoted colouration, but exogenous ABA did not. Unexpectedly, fluridone, an inhibitor of ABA biosynthesis, promoted colouration. RNA-sequencing data obtained from the four stages around ripening showed that ACO3 and NCED1/3 gene expression determined ethylene and ABA levels, respectively. Downregulation of ACO3 and NCED1/3 expression by virus-induced gene silencing (VIGS) inhibited and promoted colouration, respectively, as evidenced by changes in carotenoid, ABA, and ethylene levels, as well as carotenoid biosynthesis-related gene expression. Importantly, the retarded colouration in ACO3-VIGS fruits was rescued by exogenous ethylene.

CONCLUSIONS

Ethylene positively regulates the hot pepper fruit colouration, while inhibition of ABA biosynthesis promotes colouration, suggesting a role of ABA in de-greening. Our findings provide new insights into processes of fleshy fruit ripening regulated by ABA and ethylene, focusing on ethylene in carotenoid biosynthesis and ABA in chlorophyll degradation.

Recognition of candidate transcription factors related to bilberry fruit ripening by de novo transcriptome and qRT-PCR analyses

Bilberry (Vaccinium myrtillus L.) fruits are an excellent natural resource for human diet because of their special flavor, taste and nutritional value as well as medical properties. Bilberries are recognized for their high anthocyanin content and many of the genes involved in the anthocyanin biosynthesis have been characterized. So far, neither genomic nor RNA-seq data have been available for the species. In the present study, we de novo sequenced two bilberry fruit developmental stages, unripe green (G) and ripening (R). A total of 57,919 unigenes were assembled of which 80.2% were annotated against six public protein databases. The transcriptome served as exploratory data to identify putative transcription factors related to fruit ripening. Differentially expressed genes (DEGs) between G and R stages were prominently upregulated in R stage with the functional annotation indicating their main roles in active metabolism and catalysis. The unigenes encoding putative ripening-related regulatory genes, including members of NAC, WRKY, LOB, ERF, ARF and ABI families, were analysed by qRT-PCR at five bilberry developmental stages. Our de novo transcriptome database contributes to the understanding of the regulatory network associated with the fruit ripening in bilberry and provides the first dataset for wild Vaccinium species acquired by NGS technology.

Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria × ananassa)

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.

Jasmonate signalling pathway in strawberry: Genome-wide identification, molecular characterization and expression of JAZs and MYCs during fruit development and ripening

Jasmonates (JAs) are signalling molecules involved in stress responses, development and secondary metabolism biosynthesis, although their roles in fleshy-fruit development and ripening processes are not well known. In strawberry fruit, it has been proposed that JAs could regulate the early development through the activation of the JAs biosynthesis. Moreover, it has been reported that JA treatment increases anthocyanin content in strawberry fruit involving the bioactive jasmonate biosynthesis. Nevertheless, JA signalling pathway, of which main components are the COI1-JAZ co-receptor and the MYC transcription factors (TFs), has not been characterized in strawberry until now. Here we identified and characterized the woodland strawberry (Fragaria vesca) JAZ and MYC genes as well as studied their expression during development and ripening stages in commercial strawberry (Fragaria × ananassa) fruit. We described twelve putative JAZ proteins and two MYC TFs, which showed high conservation with respect to their orthologs in Arabidopsis thaliana and in other fleshy-fruit species such as Malus × domestica, Vitis vinifera and Solanum lycopersicum as revealed by gene synteny and phylogenetic analyses. Noteworthy, their expression levels exhibited a significant decrease from fruit development to ripening stages in F. × ananassa, along with others of the JA signalling-related genes such as FaNINJA and FaJAMs, encoding for negative regulators of JA responses. Moreover, we found that main JA signalling-related genes such as FaMYC2, and FaJAZ1 are promptly induced by JA treatment at early times in F. × ananassa fruit. These results suggest the conservation of the canonical JA signalling pathway in strawberry and a possible role of this pathway in early strawberry fruit development, which also correlates negatively with the beginning of the ripening process.

A leu-rich repeat receptor-like protein kinase, FaRIPK1, interacts with the ABA receptor, FaABAR, to regulate fruit ripening in strawberry

Strawberry (Fragaria×ananassa) is a model plant for studying non-climacteric fruit ripening regulated by abscisic acid (ABA); however, its exact molecular mechanisms are yet not fully understood. In this study, a predicted leu-rich repeat (LRR) receptor-like kinase in strawberry, red-initial protein kinase 1 (FaRIPK1), was screened and, using a yeast two-hybrid assay, was shown to interact with a putative ABA receptor, FaABAR. This association was confirmed by bimolecular fluorescence complementation and co-immunoprecipitation assays, and shown to occur in the nucleus. Expression analysis by real-time PCR showed that FaRIPK1 is expressed in roots, stems, leaves, flowers, and fruit, with a particularly high expression in white fruit at the onset of coloration. Down-regulation of FaRIPK1 expression in strawberry fruit, using Tobacco rattle virus-induced gene silencing, inhibited ripening, as evidenced by suppression of ripening-related physiological changes and reduced expression of several genes involved in softening, sugar content, pigmentation, and ABA biosynthesis and signaling. The yeast-expressed LRR and STK (serine/threonine protein kinase) domains of FaRIPK1 bound ABA and showed kinase activity, respectively. A fruit disc-incubation test revealed that FaRIPK1 expression was induced by ABA and ethylene. The synergistic action of FaRIPK1 with FaABAR in regulation of strawberry fruit ripening is discussed.

Gene expression atlas of fruit ripening and transcriptome assembly from RNA-seq data in octoploid strawberry (Fragaria × ananassa)

RNA-seq has been used to perform global expression analysis of the achene and the receptacle at four stages of fruit ripening, and of the roots and leaves of strawberry (Fragaria × ananassa). About 967 million reads and 191 Gb of sequence were produced, using Illumina sequencing. Mapping the reads in the related genome of the wild diploid Fragaria vesca revealed differences between the achene and receptacle development program, and reinforced the role played by ethylene in the ripening receptacle. For the strawberry transcriptome assembly, a de novo strategy was followed, generating separate assemblies for each of the ten tissues and stages sampled. The Trinity program was used for these assemblies, resulting in over 1.4 M isoforms. Filtering by a threshold of 0.3 FPKM, and doing Blastx (E-value < 1 e-30) against the UniProt database of plants reduced the number to 472,476 isoforms. Their assembly with the MIRA program (90% homology) resulted in 26,087 contigs. From these, 91.34 percent showed high homology to Fragaria vesca genes and 87.30 percent Fragaria iinumae (BlastN E-value < 1 e-100). Mapping back the reads on the MIRA contigs identified polymorphisms at nucleotide level, using FREEBAYES, as well as estimate their relative abundance in each sample.

A Transcriptome Approach Toward Understanding Fruit Softening in Persimmon

Persimmon (Diospyros kaki Thunb.), which is a climacteric fruit, softens in 3-5 weeks after harvest. However, little is known regarding the transcriptional changes that underlie persimmon ripening. In this study, high-throughput de novo RNA sequencing was performed to examine differential expression between freshly harvested (FH) and softened (ST) persimmon fruit peels. Using the Illumina HiSeq platform, we obtained 259,483,704 high quality reads and 94,856 transcripts. After the removal of redundant sequences, a total of 31,258 unigenes were predicted, 1,790 of which were differentially expressed between FH and ST persimmon (1,284 up-regulated and 506 down-regulated in ST compared with FH). The differentially expressed genes (DEGs) were further subjected to KEGG pathway analysis. Several pathways were found to be up-regulated in ST persimmon, including "amino sugar and nucleotide sugar metabolism." Pathways down-regulated in ST persimmon included "photosynthesis" and "carbon fixation in photosynthetic organisms." Expression patterns of genes in these pathways were further confirmed using quantitative real-time RT-PCR. Ethylene gas production during persimmon softening was monitored with gas chromatography and found to be correlated with the fruit softening. Transcription involved in ethylene biosynthesis, perception and signaling was up-regulated. On the whole, this study investigated the key genes involved in metabolic pathways of persimmon fruit softening, especially implicated in increased sugar metabolism, decreased photosynthetic capability, and increased ethylene production and other ethylene-related functions. This transcriptome analysis provides baseline information on the identity and modulation of genes involved in softening of persimmon fruits and can underpin the future development of technologies to delay softening in persimmon.